scholarly journals Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

2015 ◽  
Author(s):  
Philipp Eser ◽  
Leonhard Wachutka ◽  
Kerstin C Maier ◽  
Carina Demel ◽  
Mariana Boroni ◽  
...  
Keyword(s):  
Rna Synthesis ◽  
Model Organism ◽  
Rna Metabolism ◽  
Dna And Rna ◽  
Rna Labeling ◽  
Sequence Elements ◽  
Antisense Regulation ◽  
Kinetics Of ◽  
Synthesis And Degradation

To decrypt the regulatory code of the genome, sequence elements must be defined that determine the kinetics of RNA metabolism and thus gene expression. Here we attempt such decryption in an eukaryotic model organism, the fission yeast S. pombe. We first derive an improved genome annotation that redefines borders of 36% of expressed mRNAs and adds 487 non-coding RNAs (ncRNAs). We then combine RNA labeling in vivo with mathematical modeling to obtain rates of RNA synthesis and degradation for 5,484 expressed RNAs and splicing rates for 4,958 introns. We identify functional sequence elements in DNA and RNA that control RNA metabolic rates, and quantify the contributions of individual nucleotides to RNA synthesis, splicing, and degradation. Our approach reveals distinct kinetics of mRNA and ncRNA metabolism, separates antisense regulation by transcription interference from RNA interference, and provides a general tool for studying the regulatory code of genomes.

Cell proliferation in Allium cepa L. meristems under 8-hydroxyquinoline, a chelating agent that affects DNA and RNA polymerases

1986 ◽  
Vol 80 (1) ◽  
pp. 171-180
Author(s):  
M.L. Ferrero ◽  
C. De la Torre
Keyword(s):  
Allium Cepa ◽  
Rna Synthesis ◽  
Thymidine Incorporation ◽  
Chelating Agent ◽  
Growth Cycle ◽  
Rna Polymerases ◽  
Dna And Rna ◽  
Allium Cepa L ◽  
Nucleolar Cycle

8-Hydroxyquinoline (HQ) chelates Mg2+ and Mn2+ and, secondarily, affects the activities of DNA and RNA polymerases. The in vivo effect of HQ has been estimated in Allium cepa L. meristems growing under new growth kinetics in the presence of this agent. HQ (at both 5 X 10(−5) M and 10(−4) M) depressed incorporation of [3H]uridine much more effectively than that of [3H]-thymidine. Cycle kinetics in meristems behaved as if they were independent of the rates of synthesis or accumulation of RNA since, under HQ, cycle time was only moderately modified and the new cycle kinetics achieved could be explained by the new rates of [3H]thymidine incorporation. Lengthened S periods were partially compensated for by shortened G2 phases, suggesting that, in these cells, both the growth cycle and its coupling with the DNA-division cycle were not disturbed by a decreased amount of RNA. Finally, the nucleolar cycle during mitosis, but not the interphase nucleolus, was modified under the new rates of RNA synthesis.

«In Vivo » Studies on RNA Metabolism of Human Acute Leukemia Cells.

1965 ◽  
Vol 51 (6) ◽  
pp. 419-431 ◽  
Author(s):  
Felice Gavosto ◽  
Alessandro Pileri ◽  
Luigi Pegoraro ◽  
Wilma Gabutti
Keyword(s):  
Acute Leukemia ◽  
Degradation Products ◽  
Rna Metabolism ◽  
In Vivo Studies ◽  
Leukemia Cells ◽  
Great Stability ◽  
Blast Cells ◽  
Autoradiographic Technique ◽  
Kinetics Of

« In vivo » injection of uridine-3H was employed for the direct study of RNA metabolism in acute leukemia cells: blood samples were taken at different times following precursor administration. The degree of RNA labelling in the whole population, in some classes of blast cells with different diameter, and in the single subcellular structures was evaluated by high resolution autoradiographic technique. Great stability was observed in the RNA labelling of the blast population. This finding is discussed in relation to the following points: 1) true metabolic stability, 2) continuous intracellular resynthesis of the catabolites of the labelled macromolecules, 3) reutilization of the extracellular degradation products. From the behaviour of RNA labelling in the different classes and time-stages of the experiment some deductions about the proliferative kinetics of leukemia cells are possible. Finally from the behaviour of the labelling in the different subcellular structures (nucleus, nucleolus, cytoplasm) an early nuclear and a possible nucleolar synthesis of RNA was observed.

scholarly journals Ribosomal RNA metabolism during renal hypertrophy. Evidence of decreased degradation of newly synthesized ribosomal RNA.

1975 ◽  
Vol 64 (1) ◽  
pp. 260-265 ◽  
Author(s):  
J M Hill
Keyword(s):  
Ribosomal Rna ◽  
Rna Synthesis ◽  
Specific Activity ◽  
Rna Metabolism ◽  
Renal Hypertrophy ◽  
Degradation Rates ◽  
Kinetics Of

The degradation rates of kidney rRNA labeled before UNI or sham are unchanged 5 days after the operations (t one-and-a half, 88 h). Therefore, there is no contribution from pre-existing rRNA to the increased amount of rRNA in the stimulated kidney. After labeling with L-(methyl-3H)methionine, the kinetics of incorporation into rRNA precursors, 10-60 min and at the postoperative times of 4, 16, 36, and 96 h. The specific activity of cytoplasmic rRNA after 1-h labeling with L-(methyl-3H)methionine increased occured at 4 or 96 h. Since (a) the rate of degradation of rRNA, (b) the kinetics of incorporation and processing of rRNA precursors, and (c) the rate of RNA synthesis appear unchanged after UNI, the accretion of rRNA must involve decreased degradation of newly synthesized rRNA.

scholarly journals Dynamics of Viral RNA Synthesis during Measles Virus Infection

2005 ◽  
Vol 79 (11) ◽  
pp. 6900-6908 ◽  
Author(s):  
Sébastien Plumet ◽  
W. Paul Duprex ◽  
Denis Gerlier
Keyword(s):  
Measles Virus ◽  
Rna Synthesis ◽  
De Novo ◽  
Reference Model ◽  
Viral Rna ◽  
De Novo Synthesis ◽  
A Cell ◽  
Nucleoprotein N ◽  
Kinetics Of

ABSTRACT We propose a reference model of the kinetics of a viral RNA-dependent RNA polymerase (vRdRp) activities and its regulation during infection of eucaryotic cells. After measles virus infects a cell, mRNAs from all genes immediately start to accumulate linearly over the first 5 to 6 h and then exponentially until ∼24 h. The change from a linear to an exponential accumulation correlates with de novo synthesis of vRdRp from the incoming template. Expression of the virus nucleoprotein (N) prior to infection shifts the balance in favor of replication. Conversely, inhibition of protein synthesis by cycloheximide favors the latter. The in vivo elongation speed of the viral polymerase is ∼3 nucleotides/s. A similar profile with fivefold-slower kinetics can be obtained using a recombinant virus expressing a structurally altered polymerase. Finally, virions contain only encapsidated genomic, antigenomic, and 5′-end abortive replication fragment RNAs.

Effect of Some Metabolic Inhibitors on Vinblastine-Induced Ribosomal-Granular Material Complexes

1971 ◽  
Vol 29 ◽  
pp. 548-549
Author(s):  
Awtar Krishan ◽  
Dora Hsu
Keyword(s):  
Granular Material ◽  
Rna Synthesis ◽  
Culture Medium ◽  
Actinomycin D ◽  
Metabolic Inhibitors ◽  
Protein And Rna Synthesis ◽  
Apparent Reduction ◽  
Plant Alkaloids ◽  
In Cells

Cells exposed to antitumor plant alkaloids, vinblastine and vincristine sulfate have large proteinacious crystals and complexes of ribosomes, helical polyribosomes and electron-dense granular material (ribosomal complexes) in their cytoplasm, Binding of H3-colchicine by the in vivo crystals shows that they contain microtubular proteins. Association of ribosomal complexes with the crystals suggests that these structures may be interrelated.In the present study cultured human leukemic lymphoblasts (CCRF-CEM), were incubated with protein and RNA-synthesis inhibitors, p. fluorophenylalanine, puromycin, cycloheximide or actinomycin-D before the addition of crystal-inducing doses of vinblastine to the culture medium. None of these compounds could completely prevent the formation of the ribosomal complexes or the crystals. However, in cells pre-incubated with puromycin, cycloheximide, or actinomycin-D, a reduction in the number and size of the ribosomal complexes was seen. Large helical polyribosomes were absent in the ribosomal complexes of cells treated with puromycin, while in cells exposed to cycloheximide, there was an apparent reduction in the number of ribosomes associated with the ribosomal complexes (Fig. 2).

Effect of pH and inhibitors on beta-amyloid fibril assembly

1996 ◽  
Vol 54 ◽  
pp. 752-753
Author(s):  
Beverly E. Maleeff ◽  
Timothy K. Hart ◽  
Stephen J. Wood ◽  
Ronald Wetzel
Keyword(s):  
Amyloid Fibril ◽  
Peptide Fragment ◽  
Hydrophobic Peptides ◽  
Amyloid Fibril Formation ◽  
Effects Of Ph ◽  
Severity Of The Disease ◽  
Kinetics Of ◽  
The Brain

Alzheimer's disease is characterized post-mortem in part by abnormal extracellular neuritic plaques found in brain tissue. There appears to be a correlation between the severity of Alzheimer's dementia in vivo and the number of plaques found in particular areas of the brain. These plaques are known to be the deposition sites of fibrils of the protein β-amyloid. It is thought that if the assembly of these plaques could be inhibited, the severity of the disease would be decreased. The peptide fragment Aβ, a precursor of the p-amyloid protein, has a 40 amino acid sequence, and has been shown to be toxic to neuronal cells in culture after an aging process of several days. This toxicity corresponds to the kinetics of in vitro amyloid fibril formation. In this study, we report the biochemical and ultrastructural effects of pH and the inhibitory agent hexadecyl-N-methylpiperidinium (HMP) bromide, one of a class of ionic micellar detergents known to be capable of solubilizing hydrophobic peptides, on the in vitro assembly of the peptide fragment Aβ.

Kinetics of Various 99mTc-Sn-Pyrophosphate Compounds in the Rat

1977 ◽  
Vol 16 (04) ◽  
pp. 157-162 ◽  
Author(s):  
C. Schümichen ◽  
B. Mackenbrock ◽  
G. Hoffmann
Keyword(s):  
Normal Saline ◽  
Half Life ◽  
Compound A ◽  
Short Half Life ◽  
Low Concentrations ◽  
The Stability ◽  
Kinetics Of ◽  
In Vitro Stability

SummaryThe bone-seeking 99mTc-Sn-pyrophosphate compound (compound A) was diluted both in vitro and in vivo and proved to be unstable both in vitro and in vivo. However, stability was much better in vivo than in vitro and thus the in vitro stability of compound A after dilution in various mediums could be followed up by a consecutive evaluation of the in vivo distribution in the rat. After dilution in neutral normal saline compound A is metastable and after a short half-life it is transformed into the other 99mTc-Sn-pyrophosphate compound A is metastable and after a short half-life in bone but in the kidneys. After dilution in normal saline of low pH and in buffering solutions the stability of compound A is increased. In human plasma compound A is relatively stable but not in plasma water. When compound B is formed in a buffering solution, uptake in the kidneys and excretion in urine is lowered and blood concentration increased.It is assumed that the association of protons to compound A will increase its stability at low concentrations while that to compound B will lead to a strong protein bond in plasma. It is concluded that compound A will not be stable in vivo because of a lack of stability in the extravascular space, and that the protein bond in plasma will be a measure of its in vivo stability.

Hepatobiliary Kinetics of 113mIn-Phenolphthalexon

1981 ◽  
Vol 20 (02) ◽  
pp. 90-93
Author(s):  
P.B. Parab ◽  
U.R. Raikar ◽  
R.D. Ganatra ◽  
M. C. Patel
Keyword(s):  
Biliary Excretion ◽  
Iminodiacetic Acid ◽  
Organ Distribution ◽  
Liver Uptake ◽  
On Line ◽  
Rapid Clearance ◽  
Chemical Purity ◽  
Kinetics Of ◽  
High Liver

Phenolphthalexon, a compound with iminodiacetic acid as a functional group, has been labelled with 113mIn to high chemical purity and its usefulness in studies of biliary excretion patency has been studied. Organ distribution of 113mIn-phenolphthalexon in mice was characterized by high liver uptake (50.8% of the administered dose after 5 min) and rapid clearance through the gall bladder. An animal model for studying obstruction of biliary excretion has been developed. Data on the kinetics of the radiopharmaceutical were obtained by collecting in-vivo data through an on-line computer.

Continuous Quantitative Monitoring of Mural, Platelet-Dependent, Thrombus Kinetics in the Crushed Rat Femoral Vein

1991 ◽  
Vol 65 (04) ◽  
pp. 425-431 ◽  
Author(s):  
F Stockmans ◽  
H Deckmyn ◽  
J Gruwez ◽  
J Vermylen ◽  
R Acland
Keyword(s):  
Thrombus Formation ◽  
Femoral Vein ◽  
Maximum Size ◽  
Digital Analysis ◽  
Video Recordings ◽  
Quantitative Monitoring ◽  
Set Up ◽  
Kinetics Of ◽  
Quantitative Nature

SummaryA new in vivo method to study the size and dynamics of a growing mural thrombus was set up in the rat femoral vein. The method uses a standardized crush injury to induce a thrombus, and a newly developed transilluminator combined with digital analysis of video recordings. Thrombi in this model formed rapidly, reaching a maximum size 391 ± 35 sec following injury, after which they degraded with a half-life of 197 ± 31 sec. Histological examination indicated that the thrombi consisted mainly of platelets. The quantitative nature of the transillumination technique was demonstrated by simultaneous measurement of the incorporation of 111In labeled platelets into the thrombus. Thrombus formation, studied at 30 min interval in both femoral veins, showed satisfactory reproducibility overall and within a given animalWith this method we were able to induce a thrombus using a clinically relevant injury and to monitor continuously and reproducibly the kinetics of thrombus formation in a vessel of clinically and surgically relevant size

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